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prisms 2.4 #6

Closed
wants to merge 218 commits into from
Closed

prisms 2.4 #6

wants to merge 218 commits into from

Commits on Aug 26, 2024

  1. Updating the gold standard for precipitateEvolution

    @landinjm
    landinjm committed Aug 26, 2024
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  2. Merge pull request prisms-center#221 from prisms-center/master 

    Merge master branch into development branch
    @landinjm
    landinjm authored Aug 26, 2024
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  3. Removing old commented code

    @landinjm
    landinjm authored and landinjm committed Aug 26, 2024
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  4. Refactor of adaptiverefinement methods into a separate class. Note th… 

    …at the functionality for the initial step is slightly different because reinit() is not used.
    @landinjm
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  5. Implemented new adaptiveRefine class inplace of old refine.cc

    @landinjm
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  6. Removing old refine.cc methods

    @landinjm
    landinjm authored and landinjm committed Aug 26, 2024
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  7. Fixing autoformat on this file

    @landinjm
    landinjm committed Aug 26, 2024
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  8. Removing uneccessary variable

    @landinjm
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  9. Rearranging adaptiveRefine

    @landinjm
    landinjm committed Aug 26, 2024
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  10. optimize vtk file read-in behavior 

    Previously each vtk input would be read/parsed multiple times if it contained multiple fields. Now it will read each vtk only once. (per processor)
    @fractalsbyx
    fractalsbyx committed Aug 26, 2024
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Commits on Aug 27, 2024

  1. Adding comments and renaming some functions

    landinjm authored and landinjm committed Aug 27, 2024
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  2. Renaming function/file names

    landinjm authored and landinjm committed Aug 27, 2024
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  3. Merge remote-tracking branch 'upstream/development' into refactor_AMR

    @landinjm
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  4. Slight simplifications to the AMR criterion function

    @landinjm
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  5. Using bitwise to simplify the need values & gradients

    @landinjm
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  6. Simplification to AMR criterion loop structure

    @landinjm
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  7. Converting AMR criterion enum to allow for bitwise operations

    @landinjm
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  8. Adding comments

    @landinjm
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  9. renaming instance of AdaptiveRefinement class

    @landinjm
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  10. Spliting header file

    @landinjm
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  11. Fixing explicit instantiation

    @landinjm
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  12. Adding header to unit tests

    @landinjm
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  13. Autoformatting

    @landinjm
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  14. No need to declare extra variables 

    .
    @landinjm
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  15. Use range-based loops when appropriate 

    .

.
    @landinjm
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Commits on Aug 30, 2024

  1. Removing unused elliptic field index

    @landinjm
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  2. Removing unused parabolic field index

    @landinjm
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  3. Fixed FloodFiller unit test and added mergeSplitGrains call

    @zachcroft
    zachcroft committed Aug 30, 2024
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  4. Merge pull request prisms-center#223 from landinjm/refactor_AMR 

    Refactor adaptive meshing methods
    @landinjm
    landinjm authored Aug 30, 2024
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  5. Added check for consistent periodic BCs and unspecified BCs

    @zachcroft
    zachcroft committed Aug 30, 2024
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Commits on Sep 3, 2024

  1. using resize instead of push back

    @landinjm
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  2. Refactor whitespace deletion

    @landinjm
    landinjm committed Sep 3, 2024
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  3. switched to resize and index arrays when true

    @landinjm
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  4. Making the parse RHS more readable

    @landinjm
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  5. Making the parse LHS more readable

    @landinjm
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  6. adding ternaries

    @landinjm
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  7. Partial shift to EvaluationFlags rather than 3 separate bools

    @landinjm
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  8. Slight changes to nonlinear bool to fix unit tests

    @landinjm
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  9. Shifting postprocess to evaluation flags

    @landinjm
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  10. Moving the variable_info to evaluation flags

    @landinjm
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  11. Renaming variable

    @landinjm
    landinjm committed Sep 3, 2024
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  12. removing unused integral functions

    @landinjm
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  13. Adding evaluation flags in these files where they are hardcoded

    @landinjm
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Commits on Sep 4, 2024

  1. Merge pull request prisms-center#226 from landinjm/implicit_solvers 

    Switching to `dealii::EvaluationFlags` for deal.II 9.6.0 Compatibility
    @landinjm
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  2. missing autoformat on .hh files

    @landinjm
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  3. Merge pull request prisms-center#229 from landinjm/autoformat_hh_files 

    Missing autoformat on `*.hh` files
    @landinjm
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  4. Adding basic clang-format action

    @landinjm
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  5. Adding a few more specifications to clang-format check

    @landinjm
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  6. Basic unit test CI 

    simplications to CI with dealii docker image

more fixes

even more fixes

working
    @landinjm
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  7. removing root access

    @landinjm
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  8. unit tests run in serial in automatic tests

    @landinjm
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  9. allow mpi to run as root

    @landinjm
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  10. Adding back root access

    @landinjm
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  11. removing Travis CI

    @landinjm
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  12. updating badges

    @landinjm
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  13. slight rearrangement

    @landinjm
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  14. Merge pull request prisms-center#230 from landinjm/github_actions 

    GitHub actions
    @landinjm
    landinjm authored Sep 4, 2024
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  15. Adding vscode to gitignore

    @landinjm
    landinjm committed Sep 4, 2024
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  16. Adding python virtual environments

    @landinjm
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  17. Changed ele_val threshold to min_id

    @zachcroft
    zachcroft committed Sep 4, 2024
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  18. Merge remote-tracking branch 'upstream/development' into fix_FloodFil… 

    …l_unit_test
    @zachcroft
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  19. autoformat

    @landinjm
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  20. Merge pull request prisms-center#224 from zachcroft/fix_FloodFill_uni… 

    …t_test

Fixed FloodFiller unit test and fixed grainGrowth bug
    @landinjm
    landinjm authored Sep 4, 2024
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Commits on Sep 5, 2024

  1. Merge remote-tracking branch 'upstream/development' into pr/landinjm/232

    @landinjm
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  2. Merge pull request prisms-center#232 from landinjm/gitignore 

    Adding VS Code and venv `.gitignore`
    @landinjm
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  3. Switching to range based loops

    @landinjm
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  4. Merge pull request prisms-center#233 from landinjm/range_based_loops 

    Switching to range based loops
    @landinjm
    landinjm authored Sep 5, 2024
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Commits on Sep 8, 2024

  1. Fixes to assert in equation dependency parser

    @landinjm
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  2. Merge remote-tracking branch 'upstream/development' into fix_warnings

    @landinjm
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  3. Changed error handling to use dealii::AssertThrow()

    @zachcroft
    zachcroft committed Sep 8, 2024
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Commits on Sep 9, 2024

  1. removing deprecated applications

    @landinjm
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  2. Merge pull request prisms-center#225 from zachcroft/fix_parameter_BC_… 

    …check

Added check for consistent periodic BCs and unspecified BCs
    @landinjm
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  3. Merge pull request prisms-center#234 from landinjm/delete_deprecated_… 

    …apps

Deleting deprecated apps
    @landinjm
    landinjm authored Sep 9, 2024
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Commits on Sep 10, 2024

  1. adding overrides

    @landinjm
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  2. adding more overrides

    @landinjm
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  3. base class initialization

    @landinjm
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  4. snprintf ignore truncation

    @landinjm
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  5. missed header

    @landinjm
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  6. reorder AMR class

    @landinjm
    landinjm committed Sep 10, 2024
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  7. fixed warnings for unit tests

    @landinjm
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  8. Merge remote-tracking branch 'upstream/development' into fix_warnings

    @landinjm
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  9. fix warnings for applications

    @landinjm
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  10. unused variable

    @landinjm
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  11. Merge pull request prisms-center#235 from landinjm/fix_warnings 

    Fixed warnings & EquationDependencyParser logic
    @landinjm
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Commits on Sep 13, 2024

  1. remove deprecated tests

    @landinjm
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  2. update required deal.II version

    @landinjm
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  3. remove some old comments

    @landinjm
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  4. updating cmake requirements to reflect dealii version requirement

    @landinjm
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  5. maybe_used for allenCahn

    @ellery-hendrix
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  6. Added maybe_unused to prevent warnings.

    @gjerdej
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  7. Add unused qualifier

    Arijit Roy authored and Arijit Roy committed Sep 13, 2024
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  8. autoformat

    @landinjm
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  9. Merge pull request prisms-center#239 from arijitroy6:suppress_unused_… 

    …variables

Added `[[maybe_unused]]` variables for this application: precipitateEvolution
    @landinjm
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  10. Merge pull request prisms-center#236 from landinjm/edit_backwards_com… 

    …patability

Update backwards compatability to remove support prior to deal.II 9.2.0
    @landinjm
    landinjm authored Sep 13, 2024
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Commits on Sep 16, 2024

  1. autoformatting

    @landinjm
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  2. Merge pull request prisms-center#237 from ellery-hendrix/unused_var_c… 

    …ompiled

Added `[[maybe_unused]]` for the allenCahn applications
    @landinjm
    landinjm authored Sep 16, 2024
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  3. autoformatting

    @landinjm
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  4. Merge pull request prisms-center#238 from gjerdej/suppress_unused_var… 

    …iables

Added `[[maybe_unused]]` to prevent warnings in grainGrowth application
    @landinjm
    landinjm authored Sep 16, 2024
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  5. partially switching to unordered maps

    @landinjm
    landinjm committed Sep 16, 2024
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  6. minor optimizations

    @landinjm
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  7. finished switching to maps

    @landinjm
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  8. simplifications to variable_info struct

    @landinjm
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  9. Merge pull request prisms-center#241 from landinjm/fix_multiple_linea… 

    …r_solves

Fix multiple linear/nonlinear solves
    @landinjm
    landinjm authored Sep 16, 2024
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Commits on Sep 19, 2024

  1. dealii namespace

    @landinjm
    landinjm committed Sep 19, 2024
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  2. allenCahn warnings

    @landinjm
    landinjm committed Sep 19, 2024
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  3. allenCahn_conserved warnings

    @landinjm
    landinjm committed Sep 19, 2024
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  4. Fixed the rest of warning in debug compilation

    @landinjm
    landinjm committed Sep 19, 2024
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  5. Merge pull request prisms-center#243 from landinjm/fix_warning_applic… 

    …ation

Fixed warnings on application level
    @landinjm
    landinjm authored Sep 19, 2024
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Commits on Sep 26, 2024

  1. autoformat

    @landinjm
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  2. deleting some comments and unused variables

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    landinjm committed Sep 26, 2024
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  3. slight simplifications

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  4. slight refactor

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  5. simplifying print statements

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  6. other minor simplifications

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  7. attempt at parallel threads

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  8. Adding duplication version of apps for automatic tests

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Commits on Sep 27, 2024

  1. changes to use test version of applications instead of main directory

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  2. missed header path

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  3. Adding argparse for n threads

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Commits on Oct 1, 2024

  1. Adding system information

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  2. updating results file

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  3. Merge pull request prisms-center#247 from landinjm/update_automatic_t… 

    …est_script

Update automatic test script
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  4. initial clang-tidy file

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  5. some additions to gitignore and make file to support clangd

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  6. fixes based on clang-tidy 

    some updates to clang-tidy
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  7. Merge remote-tracking branch 'upstream/development' into clang_tidy

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  8. clang-tidy fixes

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  9. Merge pull request prisms-center#249 from landinjm/clang_tidy 

    Clang tidy fixes
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  10. Moving benchmarks

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  11. Updating makefile and header paths

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  12. moving main.cc out of each application

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  13. Merge pull request prisms-center#250 from landinjm/CHiMaD_benchmarks 

    Moving CHiMaD benchmarks & eliminating redundant `main.cc`
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  14. Adding support for 4th, 5th, and 6th order elements

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  15. Merge pull request prisms-center#251 from landinjm/CHiMaD_benchmarks 

    Adding support for 4th, 5th, and 6th order elements
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  16. fixes to header pathes

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  17. fixes to header pathes

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Commits on Oct 2, 2024

  1. Renaming CHiMaD apps

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  2. updated parameters for 1a

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  3. 1b

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  4. 1c

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  5. fix comments

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  6. Merge remote-tracking branch 'upstream/development' into pr/fractalsb… 

    …yx/222
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  7. Merge pull request prisms-center#222 from fractalsbyx/iniCond-optimiz… 

    …ation

optimize vtk file read-in behavior
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  8. Merge remote-tracking branch 'upstream/development' into pr/landinjm/252

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  9. Merge pull request prisms-center#252 from landinjm/CHiMaD_benchmarks 

    Updating CHiMaD Benchmark 1
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Commits on Oct 8, 2024

  1. fixed incomplete refactoring of methods in customPDE override

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  2. Merge pull request prisms-center#256 from landinjm/upstream_main 

    Fixed incomplete refactoring of methods in customPDE override
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Commits on Oct 14, 2024

  1. fix initialization of AMR update flags

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  2. python script to run each application in debug mode with 1 timestep

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  3. fixes to script so parameter file is copied correctly and more summar… 

    …y stats
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  4. check that integrated file exists before deleting

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  5. deleting old submission scripts

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  6. set default num of checkpoints to 0

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  7. Removing leftover integratedField.txt files

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  8. Adding pbs to gitignore

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  9. Deleting steadyStateAllenCahn

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  10. Revert "Dirichlet constraints can be distributed here" 

    This reverts commit b0f8edb.
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  11. simplifying the triangulation creation and assignment + transfinite i… 

    …nterpolation
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  12. logically issue for list output types

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  13. updating timestep with new mesh in 6b

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  14. updating debug script

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  15. Merge pull request prisms-center#245 from landinjm/check_all_applicat… 

    …ions_work

Adding script to check that all applications work
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Commits on Oct 16, 2024

  1. refactoring set time step list

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  2. fixing header

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  3. Merge pull request prisms-center#260 from landinjm/fix_log_spacing 

    Fixed log spacing
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    landinjm authored Oct 16, 2024
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  4. Adding assertions for model constants

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  5. Merge pull request prisms-center#262 from landinjm/error_handling_cus… 

    …tomPDE_constants

Adding assertions for model constants
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  6. adding markdown version of pdf

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    landinjm committed Oct 16, 2024
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  7. delete latex files

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Commits on Oct 17, 2024

  1. remove underbrace

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  2. adding back the residual terms as separate equations

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  3. rename variables in grainGrowth ICs

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  4. typo

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  5. Merge pull request prisms-center#264 from landinjm/rename_point_grain… 

    …Growth

Rename point variable in grain growth application
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Commits on Oct 18, 2024

  1. Merge pull request prisms-center#263 from landinjm/fix_typos 

    Switch to Allen-Cahn documentation to markdown
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  2. refactor implicit update

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Commits on Oct 21, 2024

  1. changed bool default initialization to true/converged

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  2. Merge pull request prisms-center#265 from landinjm/refactor_solveIncr… 

    …ement

Refactor linear/nonlinear solves in `solveIncrement.cc`
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  3. initial implicit equation implementation

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  4. test version of advection app

    @landinjm
    landinjm committed Oct 21, 2024
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  5. remove "error" message

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    landinjm committed Oct 21, 2024
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  6. reinit the solution vector for AMR

    @landinjm
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  7. add comments

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  8. conversion to map & changing var name

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  9. refactor & only storing previous time step for implicit equations

    @landinjm
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  10. adding assertions

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  11. adding assertions so old can only be specified for implicit equations

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  12. Merge remote-tracking branch 'upstream/development' into implicit_equ… 

    …ation_types
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  13. extraneous header

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  14. adding bool to variabe_info for implict equations

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Commits on Oct 22, 2024

  1. Merge pull request prisms-center#268 from landinjm/implicit_equation_… 

    …types

Support for `IMPLICIT_TIME_DEPENDENT` equation types & Advection application
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  2. add compute volume function to be passed to equations.cc and postproc… 

    …ess.cc
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  3. adding to all apps

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  4. update tests

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  5. missed some in postprocssing

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  6. adding const qualifier

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  7. missed an application

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  8. add const qualifier to missed app

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  9. Merge pull request prisms-center#269 from landinjm/compute_element_vo… 

    …lume

Method to compute element volume
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Commits on Oct 23, 2024

  1. uneccessary cmakelists

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  2. typo

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  3. Merge pull request prisms-center#271 from landinjm/update_cmake_lists 

    Removed extra `CMakeLists.txt`
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Commits on Oct 24, 2024

  1. Revert "Dirichlet constraints can be distributed here" 

    This reverts commit b0f8edb.
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Commits on Oct 25, 2024

  1. renable solution pinning

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  2. fixing function so that the use has to specify the need for pinned po… 

    …ints. Currently, pinned point is applied to all time independent and implicit fields.
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  3. deleting rigidbody unit test

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  4. adding general pinning point for parameters.prm

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  5. Merge pull request prisms-center#275 from landinjm/pinning_linear_solves 

    Pinning linear solves
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  6. wrong scope test wasn't getting reset

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Commits on Oct 26, 2024

  1. wrong scope for string declaration

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Commits on Oct 30, 2024

  1. adding 120 time limit for entire linux CI and 60 for the automatic te… 

    …st step
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  2. Merge pull request prisms-center#278 from landinjm/CI_timeout 

    Adding linux CI timeout
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Commits on Oct 31, 2024

  1. Revert "Merge pull request prisms-center#268 from landinjm/implicit_e… 

    …quation_types"

This reverts commit f97e399, reversing
changes made to 7d36387.
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  2. Merge remote-tracking branch 'origin/master' into development

    @landinjm
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  3. Merge pull request prisms-center#280 from prisms-center/development 

    2.4 Release
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Commits on Nov 1, 2024

  1. updating version changes

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  2. Update README.md with new version

    @landinjm
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Commits on Nov 2, 2024

  1. Merge branch 'master' of https://github.com/fractalsbyx/phaseField

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    fractalsbyx committed Nov 2, 2024
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